Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
DeSeq2
•
reset
0
votes
2
replies
728
views
No such file or directory DESeq2
rstudioScRNA
DESeq2
written 2.3 years ago by
DrFizz
• 0
2
votes
3
replies
3.0k
views
bulk RNA-seq analysis using R : batch effect : One question concerning Combat-seq and one question concerning DESeq2 design = batch + condition
BatchEffect
sva
DESeq2
RNASeqData
limma
updated 2.3 years ago by
James W. MacDonald
68k • written 2.3 years ago by
D-Bug
▴ 10
0
votes
1
reply
1.0k
views
DESeq2 interaction design
DESeq2
updated 2.3 years ago by
Michael Love
43k • written 2.3 years ago by
lamia11me
• 0
0
votes
1
reply
2.8k
views
DESeq2 error after installing BiocManager
scRNAseq
RStudio
DESeq2
updated 2.3 years ago by
ATpoint
★ 5.0k • written 2.3 years ago by
DrFizz
• 0
3
votes
4
replies
2.0k
views
lfcShrink() and batch effects in DESeq2
BatchEffect
lfcshrink
RNA-seq
DESeq2
2.3 years ago
Eva
▴ 10
2
votes
4
replies
1.4k
views
DESeq2 "Not full rank" and "Less than full rank" Errors with design ~ time + ind.nested + time:ind.nested
DESeq2
2.3 years ago
Erika
• 0
0
votes
1
reply
806
views
Model matrix not full rank
DESeq2
2.3 years ago
isabelle.dupanloup
• 0
1
vote
2
replies
825
views
Differential expression analysis with 7 factors (levels) at once?
DESeq2
2.3 years ago
melander
• 0
2
votes
2
replies
859
views
DESeq2: full model matrix is less than full rank
DESeq2
2.3 years ago
melander
• 0
0
votes
3
replies
4.1k
views
Difference between DESeqDataSetFromMatrix() function and DESeq() function
DESeq
DESeq2
updated 2.3 years ago by
ATpoint
★ 5.0k • written 2.3 years ago by
Abir.khazaal
▴ 10
0
votes
4
replies
1.4k
views
DESeq2 & RUVseq model matrix is less than full rank
RUVSeq
DESeq2
2.3 years ago
anne.hoffrichter
• 0
0
votes
4
replies
1.1k
views
Multi factor design and removing the effect of sex on main factor
DESeq2
2.4 years ago • updated 2.3 years ago
Mahendra
• 0
0
votes
2
replies
3.1k
views
DESeq2 discrepancy in log2FC significance and normalized counts significance
RNASeqData
DESeq2
2.3 years ago
Marina
• 0
1
vote
3
replies
1.2k
views
DESeq differential expression results are too stringet. How to relax my criteria
shrinkage
DifferentialExpression
DESeq2
updated 2.3 years ago by
ATpoint
★ 5.0k • written 2.3 years ago by
Abir.khazaal
▴ 10
0
votes
6
replies
2.0k
views
Same few genes repeated in DESeq2 Results
DESeq2
2.4 years ago
dsambo
▴ 10
0
votes
5
replies
1.4k
views
DESeq2 analysis
DESe
DESeq2
2.4 years ago • updated 2.3 years ago
Adèle
• 0
4
votes
9
replies
3.7k
views
RNA seq differential expression analysis for large sample size
edgeR
DESeq2
2.4 years ago
Luca
• 0
0
votes
1
reply
705
views
Using DEseq2 for two conditions with different dispersions
DESeq2
updated 2.4 years ago by
Michael Love
43k • written 2.4 years ago by
adi.rotem
• 0
0
votes
0
replies
831
views
Can't get working R 3.6.3 and 4.2.3 with DESEq2 if compiled by AMD CLANG at Ubuntu 22.04 x64
CLANG
DESeq2
2.4 years ago
lokapal
• 0
1
vote
2
replies
907
views
I changed the reference in DGE contrasts by DESeq2, but the results changed just a bit and not in the sign of Log2FC (positive to negative and invers…
RNASeqData
DESeq2
updated 2.4 years ago by
Michael Love
43k • written 2.4 years ago by
mohammad.hossein.banabazi
• 0
0
votes
8
replies
1.4k
views
Deseq2 Results are different using batch design
DESeq2
2.4 years ago
hemantcnaik
• 0
1
vote
2
replies
828
views
Building Multifactor Model in DESeq2
DESeq2
2.4 years ago
Abhishek Singh
▴ 20
0
votes
11
replies
3.1k
views
Unable to install DESeq2
DESeq2
updated 2.4 years ago by
James W. MacDonald
68k • written 2.4 years ago by
luis.franco
• 0
0
votes
2
replies
1.3k
views
Correct DESeq2 design for tumoral stage differences in tumoral and matched-normal samples
DifferentialExpression
RNASeq
DESeq2
2.4 years ago
Matteo
• 0
0
votes
2
replies
1.8k
views
Creating heatmaps with 2 Log Fold Changes in DESEQ2
DESeq2
written 2.4 years ago by
bio2249
• 0
0
votes
1
reply
612
views
Tximport - Is transcript level expression sum equal to summarisetogene() results
tximpor
DESeq2
updated 2.4 years ago by
Michael Love
43k • written 2.4 years ago by
Anshu
• 0
1
vote
2
replies
920
views
DGE analysis for diseased samples through DESeq2 and Ballgown
DESeq2
DGEanalysis
ballgown
Ballgown
DiseasedvsNormal
2.4 years ago
Bushra
• 0
0
votes
4
replies
1.4k
views
lfc direction of effect flipped for ashr, apeGLM, but accurate to biological data for non-shrunken
DESeq2
apeglm
DESeq
ApeGLM
Ashr
updated 2.4 years ago by
Michael Love
43k • written 2.4 years ago by
Ndimensional
▴ 20
0
votes
1
reply
1.2k
views
Specifying design in DESeqDataSetFromMatrix
DESeq2
updated 2.4 years ago by
ATpoint
★ 5.0k • written 2.4 years ago by
MaXXinE
• 0
1
vote
1
reply
1.6k
views
DESeq2 LRT Reduced Formula
DESeq2
updated 2.4 years ago by
James W. MacDonald
68k • written 2.4 years ago by
austinma
• 0
0
votes
2
replies
558
views
Complex DESeq2 Experimental Design
DESEq2
DESeq2
updated 2.4 years ago by
James W. MacDonald
68k • written 2.4 years ago by
Elizabeth
• 0
1
vote
9
replies
1.5k
views
DESeq2 not replicable results
RNASeqData
DESeq2
updated 2.4 years ago by
Michael Love
43k • written 2.4 years ago by
Matteo
• 0
0
votes
3
replies
915
views
p-value<0.05 for a gene with zero counts?
DESeq2
updated 2.4 years ago by
Michael Love
43k • written 2.4 years ago by
andrebolerbarros
▴ 20
2
votes
1
reply
726
views
Running DEseq2 without "factor" gives unexpected results
DESeq2
updated 2.4 years ago by
James W. MacDonald
68k • written 2.4 years ago by
adi.rotem
• 0
2
votes
1
reply
1.3k
views
DESeq2 time course using fitted splines
RNASeqData
TimeCourse
DESeq2
timecoursedata
updated 17 months ago by
Michael Love
43k • written 2.4 years ago by
georgii.vdovin
• 0
4
votes
5
replies
3.9k
views
DESeq2, time-course interpretation
Transcriptomics
TimeCourse
DESeq2
updated 2.4 years ago by
Michael Love
43k • written 2.4 years ago by
smac_head
• 0
7
votes
3
replies
1.7k
views
Proper way to implement DESeq2 when comparing samples with trisomies?
DESeq2
updated 2.4 years ago by
Michael Love
43k • written 2.4 years ago by
Kathleen Reed
▴ 20
0
votes
3
replies
1.6k
views
Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison
DESeq2
Genetics
contrasts
RNASeq
updated 2.4 years ago by
James W. MacDonald
68k • written 2.4 years ago by
a26fd14e
• 0
0
votes
1
reply
965
views
Controlling for covariates and identifying DEGs using DESeq2
RNASeqData
DESeq2
updated 2.4 years ago by
Michael Love
43k • written 2.4 years ago by
Abhishek Singh
▴ 20
8
votes
7
replies
3.1k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2
glmGamPoi
DEXSeq
updated 2.4 years ago by
alexandresegers
▴ 20 • written 3.1 years ago by
jeremymsimon
▴ 20
1
vote
8
replies
2.6k
views
DESeq2 test for synergistic vs additive effects
synergistic
additive
DESeq2
updated 20 months ago by
Wolfgang Huber
★ 13k • written 2.4 years ago by
Jane
▴ 10
2
votes
9
replies
2.4k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport
tximportData
DESeq2
2.4 years ago
Ndimensional
▴ 20
2
votes
3
replies
1.9k
views
Identify highly variable genes after vst
DESeq2
updated 2.4 years ago by
ATpoint
★ 5.0k • written 2.4 years ago by
MaXXinE
• 0
0
votes
5
replies
1.9k
views
DESeq2 design formula
designformula
DESeq2
updated 2.4 years ago by
swbarnes2
★ 1.4k • written 2.4 years ago by
Grace.Ciabattoni
• 0
0
votes
1
reply
1.2k
views
really low padj value from DESeq2
DESeq2
updated 2.4 years ago by
ATpoint
★ 5.0k • written 2.4 years ago by
Sara
• 0
1
vote
1
reply
1.0k
views
DESEQ2 differential expression for subsets of data?
RNASeqData
DESeq2
updated 2.4 years ago by
ATpoint
★ 5.0k • written 2.4 years ago by
amnahsiddiqa
▴ 10
0
votes
2
replies
914
views
plotCounts label each sample
p
DESeq2
updated 2.4 years ago by
ATpoint
★ 5.0k • written 2.4 years ago by
claire
• 0
0
votes
2
replies
1.3k
views
Heat Map
ColData
pheatmap
DESeq2
written 2.4 years ago by
dania.khalid
• 0
1
vote
6
replies
3.2k
views
Choosing between VST and rlog for PCA for outlier identification in DESeq2 when small number of samples
DESeq2
updated 2.4 years ago by
ATpoint
★ 5.0k • written 2.4 years ago by
nisreen.khambati
• 0
0
votes
3
replies
1.1k
views
Normalization of different input materials
Normalization
DESeq2
updated 2.4 years ago by
ATpoint
★ 5.0k • written 2.4 years ago by
altuda
▴ 10
4,840 results • Page
11 of 97
Recent ...
Replies
Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study
by
ATpoint
★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR
by
efoss
▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma
by
Gordon Smyth
53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
by
Ahmed Salah
• 0
Thank you very much! will take that into consideration
Votes
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Awards
• All
Popular Question
to
Hervé Pagès
16k
Popular Question
to
jared.andrews07
▴ 30
Popular Question
to
James W. MacDonald
68k
Popular Question
to
shepherl
4.2k
Popular Question
to
Gordon Smyth
53k
Locations
• All
United States,
6 minutes ago
United States,
11 minutes ago
Seattle, WA, United States,
52 minutes ago
United States,
1 hour ago
United States,
1 hour ago
Traffic: 529 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6